8RAX | pdb_00008rax

The crystal structure of DNA-bound human MutSbeta (MSH2_G674D/MSH3) in the canonical mismatch bound conformation, nucleotide free

• PDB DOI: https://doi.org/10.2210/pdb8RAX/pdb
• NAKB: 8RAX

• Classification: DNA BINDING PROTEIN
• Organism(s): Homo sapiens, synthetic construct
• Expression System: Spodoptera frugiperda
• Mutation(s): Yes 


• Deposited: 2023-12-01 Released: 2025-06-11 
• Deposition Author(s): Thomsen, M., Neudegger, T., Thieulin-Pardo, G., Blaesse, M., Costanzi, E., Steinbacher, S., Plotnikov, N.V., Dominguez, C., Iyer, R.R., Wilkinson, H.A., Monteagudo, E., Haque, T.S., Prasad, B.C., Finley, M., Boudet, J., Vogt, T.F., Felsenfeld, D.P.
• Funding Organization(s): CHDI Foundation

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.16 Å
• R-Value Free: 
  0.292 (Depositor), 0.286 (DCC) 
• R-Value Work: 
  0.257 (Depositor), 0.255 (DCC) 
• R-Value Observed: 
  0.259 (Depositor) 

Starting Model: experimental

Literature

The crystal structure of DNA-bound human MutSbeta (MSH2/MSH3) in the canonical mismatch bound conformation with ADP bound in MSH2 and MSH3

Thomsen, M., Neudegger, T., Thieulin-Pardo, G., Blaesse, M., Costanzi, E., Steinbacher, S., Plotnikov, N.V., Dominguez, C., Iyer, R.R., Wilkinson, H.A., Monteagudo, E., Haque, T.S., Prasad, B.C., Finley, M., Boudet, J., Vogt, T.F., Felsenfeld, D.P.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 Pseudo Symmetry: Cyclic - C2  (Explore in 3D)
Pseudo Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 223.93 kDa 
• Atom Count: 13,983 
• Modeled Residue Count: 1,684 
• Deposited Residue Count: 1,900 
• Unique protein chains: 2
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA mismatch repair protein Msh2	A	934	Homo sapiens	Mutation(s): 1  Gene Names: MSH2
UniProt & NIH Common Fund Data Resources
Find proteins for P43246 (Homo sapiens) Explore P43246  Go to UniProtKB:  P43246
PHAROS:  P43246 GTEx:  ENSG00000095002

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA mismatch repair protein Msh3	B	918	Homo sapiens	Mutation(s): 0  Gene Names: MSH3
UniProt & NIH Common Fund Data Resources
Find proteins for P20585 (Homo sapiens) Explore P20585  Go to UniProtKB:  P20585
PHAROS:  P20585 GTEx:  ENSG00000113318

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*AP*TP*CP*TP*GP*AP*AP*GP*CP*CP*GP*AP*TP*CP*GP*AP*TP*G)-3')	C	24	synthetic construct

Entity ID: 4
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*TP*CP*AP*TP*CP*GP*AP*TP*CP*GP*CP*AP*GP*CP*TP*TP*CP*AP*GP*AP*TP*A)-3')	D	24	synthetic construct

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.16 Å
• R-Value Free:  0.292 (Depositor), 0.286 (DCC) 
• R-Value Work:  0.257 (Depositor), 0.255 (DCC) 
• R-Value Observed: 0.259 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.899	α = 67.68
b = 90.998	β = 86.73
c = 96.162	γ = 73.86

Software Package:

Software Name	Purpose
REFMAC	refinement
autoPROC	data reduction
autoPROC	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-06-11 
Deposition Author(s): Thomsen, M., Neudegger, T., Thieulin-Pardo, G., Blaesse, M., Costanzi, E., Steinbacher, S., Plotnikov, N.V., Dominguez, C., Iyer, R.R., Wilkinson, H.A., Monteagudo, E., Haque, T.S., Prasad, B.C., Finley, M., Boudet, J., Vogt, T.F., Felsenfeld, D.P.

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Funding Organization	Location	Grant Number
CHDI Foundation	United States	--

Revision History  

• Version 1.0: 2025-06-11
  Type: Initial release
  
• Version 1.1: 2025-07-09
  Changes: Structure summary